Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Common
common (popmax 35.8%, sas) — too common for a highly-penetrant pathogenic allele
Conditions
1
dyskeratosis congenita, X-linked
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.6 | GERP -2.6 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 0.172 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
35.8%
South Asian · 19,706/54,986 alleles
Filtering AF
35.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 35.2%
Overall
10.7%
126,755/1,182,442 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 35.8% | 3 |
| Middle Eastern | 23.9% | 4 |
| Admixed American | 23.5% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 19.5% | 5 |
| Remaining individualsnot grpmax-eligible | 12.7% | 8 |
| Amishnot grpmax-eligible | 11.5% | 9 |
| European (non-Finnish) | 8.98% | 11 |
| Finnishnot grpmax-eligible | 6.86% | 15 |
| East Asian | 6.82% | 15 |
| African / African-American | 2.6% | 38 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DKC1
- Coding
- c.*6G>A
- MANE Select
- NM_001363
- dbSNP
- rs1800533
- Type
- single nucleotide variant
- Location
- chrX:154776873 (GRCh38)
- Structure
- AlphaFold pLDDT 79.74 · 7 PDB
Similar variants
- DKC1 p.Ala353Val Pathogenic ★★ ⚠ same condition
- DKC1 p.Ile38Met Likely pathogenic ★★ ⚠ same condition
- DKC1 p.Thr49Met Pathogenic ★★ ⚠ same condition
- DKC1 p.Thr66Ala Pathogenic/Likely pathogenic ★★ ⚠ same condition
- DKC1 p.Gln414Glu Uncertain significance ★★ ⚠ same condition
- DKC1 p.Glu440Lys Uncertain significance ★★ ⚠ same condition
- DKC1 p.Ile163Leu Uncertain significance ★★ ⚠ same condition
- DKC1 p.Ile187Leu Uncertain significance ★★ ⚠ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dkc1-c-star-6g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown